Heatmap

Number of Genes

Raf

Volcano Plot of Significant Genes

Volcano Plot of All Expressed Genes

Enrichments with EnrichR

Upregulated in Mutant

## Uploading data to Enrichr... Done.
##   Querying GO_Biological_Process_2018... Done.
##   Querying KEGG_2019... Done.
## Parsing results... Done.

Downregulated in Mutant

## Uploading data to Enrichr... Done.
##   Querying GO_Biological_Process_2018... Done.
##   Querying KEGG_2019... Done.
## Parsing results... Done.

GSEA Analysis

clusterProfiler

Using MSigDB C5

Pathway Visualisation

Toll Signalling Pathway

MAPK Signalling Pathway

Dorsal Target Genes

Dorsal Targets in the Mesoderm

Hypergeometric Test

q = nrow(zscores_meso)
m = nrow(zscores_meso)
n = nrow(counts(dds)) - nrow(zscores_meso)
k = nrow(ue)
  
phyper(q, m, n, k, lower.tail = FALSE)
## [1] 0

Dorsal Targets in the Neuroectoderm

Hypergeometric Test

q = nrow(zscores_neuroecto)
m = nrow(zscores_neuroecto)
n = nrow(counts(dds)) - nrow(ue)
k = nrow(ue)
  
phyper(q, m, n, k, lower.tail = FALSE)
## [1] 0

Dorsal Targets in the Ectoderm

Hypergeometric Test

q = nrow(zscores_ecto) - 1
m = nrow(zscores_ecto)
n = nrow(counts(dds)) - nrow(oe)
k = nrow(oe)
  
phyper(q, m, n, k, lower.tail = FALSE)
## [1] 4.643589e-05

Combined Heatmap

Session Info

## R version 4.1.1 (2021-08-10)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
##  [1] grid      parallel  stats4    stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] png_0.1-7                             VennDiagram_1.6.20                   
##  [3] futile.logger_1.4.3                   enrichR_3.0                          
##  [5] pathview_1.32.0                       org.Dm.eg.db_3.13.0                  
##  [7] msigdbr_7.4.1                         ggrepel_0.9.1                        
##  [9] cowplot_1.1.1                         ggpubr_0.4.0                         
## [11] data.table_1.14.0                     DT_0.19                              
## [13] forcats_0.5.1                         dplyr_1.0.7                          
## [15] purrr_0.3.4                           readr_2.0.1                          
## [17] tidyr_1.1.3                           tibble_3.1.4                         
## [19] ggplot2_3.3.5                         tidyverse_1.3.1                      
## [21] stringr_1.4.0                         clusterProfiler_4.0.5                
## [23] BSgenome.Dmelanogaster.UCSC.dm6_1.4.1 BSgenome_1.60.0                      
## [25] rtracklayer_1.52.1                    Biostrings_2.60.2                    
## [27] XVector_0.32.0                        pheatmap_1.0.12                      
## [29] geneplotter_1.70.0                    annotate_1.70.0                      
## [31] XML_3.99-0.7                          reshape_0.8.8                        
## [33] lattice_0.20-44                       gridExtra_2.3                        
## [35] RColorBrewer_1.1-2                    GenomicFeatures_1.44.2               
## [37] AnnotationDbi_1.54.1                  knitr_1.33                           
## [39] DESeq2_1.32.0                         SummarizedExperiment_1.22.0          
## [41] Biobase_2.52.0                        MatrixGenerics_1.4.3                 
## [43] matrixStats_0.60.1                    GenomicRanges_1.44.0                 
## [45] GenomeInfoDb_1.28.4                   IRanges_2.26.0                       
## [47] S4Vectors_0.30.0                      BiocGenerics_0.38.0                  
## 
## loaded via a namespace (and not attached):
##   [1] utf8_1.2.2               tidyselect_1.1.1         RSQLite_2.2.8           
##   [4] htmlwidgets_1.5.4        BiocParallel_1.26.2      scatterpie_0.1.7        
##   [7] munsell_0.5.0            withr_2.4.2              colorspace_2.0-2        
##  [10] GOSemSim_2.18.1          filelock_1.0.2           highr_0.9               
##  [13] rstudioapi_0.13          ggsignif_0.6.2           DOSE_3.18.2             
##  [16] labeling_0.4.2           KEGGgraph_1.52.0         GenomeInfoDbData_1.2.6  
##  [19] polyclip_1.10-0          bit64_4.0.5              farver_2.1.0            
##  [22] rprojroot_2.0.2          downloader_0.4           vctrs_0.3.8             
##  [25] treeio_1.16.2            generics_0.1.0           lambda.r_1.2.4          
##  [28] xfun_0.25                BiocFileCache_2.0.0      R6_2.5.1                
##  [31] graphlayouts_0.7.1       locfit_1.5-9.4           bitops_1.0-7            
##  [34] cachem_1.0.6             fgsea_1.18.0             gridGraphics_0.5-1      
##  [37] DelayedArray_0.18.0      assertthat_0.2.1         BiocIO_1.2.0            
##  [40] scales_1.1.1             ggraph_2.0.5             enrichplot_1.12.2       
##  [43] gtable_0.3.0             tidygraph_1.2.0          rlang_0.4.11            
##  [46] genefilter_1.74.0        splines_4.1.1            rstatix_0.7.0           
##  [49] lazyeval_0.2.2           broom_0.7.9              abind_1.4-5             
##  [52] yaml_2.2.1               reshape2_1.4.4           modelr_0.1.8            
##  [55] crosstalk_1.1.1          backports_1.2.1          qvalue_2.24.0           
##  [58] tools_4.1.1              ggplotify_0.1.0          ellipsis_0.3.2          
##  [61] jquerylib_0.1.4          Rcpp_1.0.7               plyr_1.8.6              
##  [64] progress_1.2.2           zlibbioc_1.38.0          RCurl_1.98-1.4          
##  [67] prettyunits_1.1.1        viridis_0.6.1            haven_2.4.3             
##  [70] fs_1.5.0                 magrittr_2.0.1           futile.options_1.0.1    
##  [73] DO.db_2.9                openxlsx_4.2.4           reprex_2.0.1            
##  [76] hms_1.1.0                patchwork_1.1.1          evaluate_0.14           
##  [79] xtable_1.8-4             rio_0.5.27               readxl_1.3.1            
##  [82] compiler_4.1.1           biomaRt_2.48.3           crayon_1.4.1            
##  [85] shadowtext_0.0.9         htmltools_0.5.2          ggfun_0.0.4             
##  [88] tzdb_0.1.2               aplot_0.1.1              lubridate_1.7.10        
##  [91] DBI_1.1.1                formatR_1.11             tweenr_1.0.2            
##  [94] dbplyr_2.1.1             MASS_7.3-54              rappdirs_0.3.3          
##  [97] babelgene_21.4           Matrix_1.3-4             car_3.0-11              
## [100] cli_3.0.1                igraph_1.2.6             pkgconfig_2.0.3         
## [103] GenomicAlignments_1.28.0 foreign_0.8-81           xml2_1.3.2              
## [106] ggtree_3.0.4             rvest_1.0.1              yulab.utils_0.0.2       
## [109] digest_0.6.27            graph_1.70.0             rmarkdown_2.10          
## [112] cellranger_1.1.0         fastmatch_1.1-3          tidytree_0.3.5          
## [115] restfulr_0.0.13          curl_4.3.2               Rsamtools_2.8.0         
## [118] rjson_0.2.20             lifecycle_1.0.0          nlme_3.1-152            
## [121] jsonlite_1.7.2           carData_3.0-4            viridisLite_0.4.0       
## [124] fansi_0.5.0              pillar_1.6.2             KEGGREST_1.32.0         
## [127] fastmap_1.1.0            httr_1.4.2               survival_3.2-11         
## [130] GO.db_3.13.0             glue_1.4.2               zip_2.2.0               
## [133] Rgraphviz_2.36.0         bit_4.0.4                ggforce_0.3.3           
## [136] stringi_1.7.4            blob_1.2.2               org.Hs.eg.db_3.13.0     
## [139] memoise_2.0.0            ape_5.5